Problem in using FEM tool

Discussions
1

Hi,

I want to use FEM tool. I am following the fem_tool_doc provided with the FEM tool. However, I didn’t see any option in Brainstorm window to use FEM tool. I found BEM tool but I would like to use FEM.

Please, show me the way how to use FEM tool.

Thanks in advance.
Bashar

2

Hello,

the FEM tool is distributed with BrainStorm but runs separately, hence there is no GUI connexion between the 2 so far; Following the directions in the documentation should help you run the FEMTool just fine.

Please let us know in case not.

3

Hi Sylvain,

Thank you very much for your information regarding FEM tool. However, I want to use 4 or 5 layered sphere and to assign conductivity to each tetrahedra. Perhaps, such types of features are absent in this tool. Then how can I use this FEM tool to satisfy my requirements?

Thank in advance.
Bashar

4

I am sorry but I think the FEM tool is limited to either a 3-shell spherical model or a realistic geometry that may be warped to the individual anatomy.

5

Dear Sylvain,

Thank you very much for your information. If I want to use spherical model, then how can I feed the spehere information (radius or center) to FEM tool? As FEM is used to process piecewise element, so how can I assign conductivities to each element?

Regards
Bashar

6

You actually can work with a 5 layer model. All you have to do is to create a 5 layered image first.

If you take a look at the “example_label.mat” file in the examples directory of the tool, you can see how the data structure of this label file is organized. Essentially its a 3D matlab array (“V”), where each voxel represents a label value and a vector for the actual voxel size (“vox_siz”). If you create a 5 layer sphere voxel image, you should be able to import it into the tool and segment it.

Here is an example:

V=zeros(256,256,256);
vox_siz=[1 1 1];

for i=1:256
for j=1:256
for k=1:256
r=sqrt((i-128)^2+(j-128)^2+(k-128)^2);
if(r<10)
V(i,j,k)=1;
end
if(r<8)
V(i,j,k)=2;
end
if(r<6)
V(i,j,k)=3;
end
if(r<4)
V(i,j,k)=4;
end
if(r<3)
V(i,j,k)=5;
end

end
end
end

save V vox_size my5layer_sphere.mat

Make sure you are somewhat generous with the layer-thickness, so the tessellation algorithm wont have to squeeze in to many tiny tetrahedrons.

7

Hi,

Thank you very much for your sample coding. I shall try with your provided coding and instruction. I have another question that is, how can I assign conductivity tensor (anisotropic conductivity) or conductivity vector (inhomogeneous cases) to each tetrahedra? When I have followed the provided guideline, I have assigned conductivities per label. But I intend to assign conductivities per element.

I am looking forward to hearing your response.

Regards
Bashar